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JuliaStats · Dec 5, 2017 · 37d82e2 · 37d82e2
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diff --git a/docs/jmd/constructors.jmd b/docs/jmd/constructors.jmd
@@ -11,10 +11,10 @@ lmm
 For illustration, several data sets from the *lme4* package for *R* are made available in `.rda` format in this package.
 These include the `Dyestuff` and `Dyestuff2` data sets.
 ```{julia;term=true}
-using DataFrames, RData, MixedModels
+using DataFrames, RData, MixedModels, StatsBase
 const dat = convert(Dict{Symbol,DataFrame},
     load(Pkg.dir("MixedModels", "test", "dat.rda")));
-dump(dat[:Dyestuff])
+describe(dat[:Dyestuff])
 ```
 The columns in these data sets have been renamed for convenience.
 The response is always named `Y`.

diff --git a/docs/src/SubjectItem.md b/docs/src/SubjectItem.md
@@ -11,40 +11,40 @@ julia> const dat = convert(Dict{Symbol,DataFrame}, load(Pkg.dir("MixedModels", "
 julia> mm1 = fit!(lmm(@formula(Y ~ 1+S+T+U+V+W+X+Z+(1+S+T+U+V+W+X+Z|G)+(1+S+T+U+V+W+X+Z|H)), dat[:kb07]))
 Linear mixed model fit by maximum likelihood
  Formula: Y ~ 1 + S + T + U + V + W + X + Z + ((1 + S + T + U + V + W + X + Z) | G) + ((1 + S + T + U + V + W + X + Z) | H)
-     logLik        -2 logLik          AIC             BIC       
- -1.42931613×10⁴  2.85863226×10⁴  2.87483226×10⁴  2.91930103×10⁴
+     logLik       -2 logLik         AIC            BIC      
+ -1.4293159×10⁴  2.8586318×10⁴  2.8748318×10⁴ 2.91930056×10⁴
 
 Variance components:
               Column     Variance   Std.Dev.    Corr.
- G        (Intercept)   90791.6237 301.316484
-          S              5187.9402  72.027357 -0.43
-          T              5552.4111  74.514503 -0.47  0.07
-          U              7584.6653  87.089984  0.21 -0.20  0.41
-          V              8841.5313  94.029417  0.20 -0.76 -0.54 -0.20
-          W              1823.9330  42.707529  0.47 -0.53 -0.11 -0.44  0.29
-          X              7422.6234  86.154648 -0.10  0.13 -0.05 -0.86 -0.06  0.70
-          Z              3801.2195  61.654031 -0.48  0.41 -0.38 -0.09  0.18 -0.78 -0.39
- H        (Intercept)  130031.4034 360.598674
-          S              1853.0405  43.046957 -0.34
-          T             62466.7444 249.933480 -0.68 -0.45
-          U              2941.3214  54.233950  0.20 -0.06 -0.18
-          V              1037.6157  32.212044  0.57 -0.75  0.02  0.02
-          W              1619.1082  40.238144  0.28 -0.04 -0.27  0.44 -0.21
-          X              4706.3361  68.602741  0.08 -0.24  0.21 -0.13 -0.26  0.01
-          Z              4837.5738  69.552669  0.04 -0.45  0.32 -0.69  0.65 -0.68 -0.10
- Residual              399587.7869 632.129565
+ G        (Intercept)   90715.0184 301.189340
+          S              5180.3901  71.974927 -0.43
+          T              5543.1348  74.452232 -0.47  0.08
+          U              7584.8816  87.091226  0.21 -0.20  0.41
+          V              8832.9843  93.983958  0.20 -0.76 -0.54 -0.20
+          W              1821.9809  42.684668  0.47 -0.53 -0.11 -0.44  0.28
+          X              7417.1453  86.122850 -0.10  0.13 -0.05 -0.86 -0.06  0.70
+          Z              3801.0318  61.652509 -0.47  0.41 -0.39 -0.09  0.18 -0.78 -0.39
+ H        (Intercept)  129690.6871 360.125932
+          S              1856.9765  43.092650 -0.34
+          T             62370.7020 249.741270 -0.68 -0.45
+          U              2950.1553  54.315332  0.20 -0.03 -0.18
+          V              1042.0598  32.280950  0.57 -0.76  0.02  0.02
+          W              1620.5108  40.255569  0.28 -0.03 -0.27  0.44 -0.21
+          X              4703.6870  68.583431  0.08 -0.24  0.21 -0.13 -0.26  0.02
+          Z              4821.2335  69.435103  0.04 -0.47  0.32 -0.68  0.65 -0.69 -0.10
+ Residual              399627.0136 632.160592
  Number of obs: 1790; levels of grouping factors: 56, 32
 
   Fixed-effects parameters:
              Estimate Std.Error  z value P(>|z|)
-(Intercept)   2180.63   76.8637  28.3701  <1e-99
-S            -66.9899   19.3343 -3.46482  0.0005
-T            -333.881   47.6917 -7.00082  <1e-11
-U             78.9861   21.2279  3.72087  0.0002
-V             22.1509   20.3366  1.08922  0.2761
-W            -18.9244   17.5052 -1.08107  0.2797
-X             5.26196   22.4251 0.234646  0.8145
-Z            -23.9501   21.0314 -1.13878  0.2548
+(Intercept)   2180.63   76.7856  28.3989  <1e-99
+S              -66.99   19.3346 -3.46478  0.0005
+T            -333.881   47.6587 -7.00566  <1e-11
+U              78.987    21.235  3.71967  0.0002
+V             22.1518   20.3368  1.08925  0.2760
+W            -18.9243   17.5061 -1.08101  0.2797
+X             5.26182   22.4216 0.234677  0.8145
+Z             -23.951   21.0197 -1.13946  0.2545
 
 
 ````
@@ -65,9 +65,9 @@ xtol_abs:                 [1.0e-10, 1.0e-10, 1.0e-10, 1.0e-10, 1.0e-10, 1.0e-10,
 initial_step:             [0.75, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 0.75, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 0.75, 1.0, 1.0, 1.0, 1.0, 1.0, 0.75, 1.0, 1.0, 1.0, 1.0, 0.75, 1.0, 1.0, 1.0, 0.75, 1.0, 1.0, 0.75, 1.0, 0.75, 0.75, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 0.75, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 0.75, 1.0, 1.0, 1.0, 1.0, 1.0, 0.75, 1.0, 1.0, 1.0, 1.0, 0.75, 1.0, 1.0, 1.0, 0.75, 1.0, 1.0, 0.75, 1.0, 0.75]
 maxfeval:                 -1
 
-Function evaluations:     2150
-Final parameter vector:   [0.476669, -0.0495603, -0.0559578, 0.0294869, 0.0291771, 0.0319766, -0.0139779, -0.0464195, 0.102601, -0.0172312, -0.0166362, -0.110942, -0.0244482, 0.0126322, 0.0219091, 0.102309, 0.0780709, -0.0945351, 0.00503189, -0.0133206, -0.0649625, 0.108351, 0.00551326, -0.0540187, -0.134323, 0.0515467, 0.0, 0.000989713, 0.00082312, -0.000902588, 0.0, 0.00013651, -0.000244137, 0.0, 6.27183e-9, 0.0, 0.570451, -0.0233509, -0.267494, 0.0174073, 0.0289346, 0.0178525, 0.00842305, 0.00494545, 0.0639696, -0.288241, 0.00128561, -0.0302377, 0.00360149, -0.0252118, -0.050996, 0.0411303, -0.0300041, -0.0137795, -0.0247621, 0.0957016, 0.0127431, 0.07846, -0.0102507, 0.0172816, 0.0193387, -0.0779396, 0.0234571, -0.0529219, -0.0391965, 0.0569404, 0.00277857, -0.00149982, -0.00147603, 0.0, -4.42426e-5, 0.0]
-Final objective value:    28586.322643859592
+Function evaluations:     2829
+Final parameter vector:   [0.476444, -0.0495227, -0.0557742, 0.0295214, 0.0292097, 0.0319541, -0.0139336, -0.0463229, 0.102521, -0.0170701, -0.0165868, -0.110967, -0.0243266, 0.0126983, 0.0218126, 0.102316, 0.0781059, -0.0943707, 0.00505476, -0.0135029, -0.0650083, 0.108318, 0.00550319, -0.0540444, -0.134248, 0.0516112, 0.0, 0.000111037, 9.89607e-5, -0.000120772, 0.0, 0.000144849, -0.000171985, 0.0, 1.49074e-5, 0.0, 0.569675, -0.0234122, -0.266913, 0.0173413, 0.0290032, 0.0178621, 0.00844082, 0.0049074, 0.0640206, -0.288127, 0.00329602, -0.0307006, 0.00437284, -0.0241439, -0.053426, 0.0425733, -0.0139551, -0.0162798, -0.0184925, 0.0991966, -0.00479098, 0.0829213, -0.00678668, 0.0223168, 0.000985977, -0.0775749, 0.0226446, -0.0535127, -0.0355039, 0.0560694, 0.00364195, -0.00381326, -0.00114592, 0.0, -5.49465e-5, 0.0]
+Final objective value:    28586.31798310179
 Return code:              FTOL_REACHED
 
 
@@ -77,31 +77,31 @@ Return code:              FTOL_REACHED
 
 ````julia
 julia> mm1.trms[1].Λ
-8×8 Array{Float64,2}:
-  0.476669    0.0         0.0          0.0          0.0           0.0          0.0         0.0
- -0.0495603   0.102601    0.0          0.0          0.0           0.0          0.0         0.0
- -0.0559578  -0.0172312   0.102309     0.0          0.0           0.0          0.0         0.0
-  0.0294869  -0.0166362   0.0780709    0.108351     0.0           0.0          0.0         0.0
-  0.0291771  -0.110942   -0.0945351    0.00551326   0.0           0.0          0.0         0.0
-  0.0319766  -0.0244482   0.00503189  -0.0540187    0.000989713   0.0          0.0         0.0
- -0.0139779   0.0126322  -0.0133206   -0.134323     0.00082312    0.00013651   0.0         0.0
- -0.0464195   0.0219091  -0.0649625    0.0515467   -0.000902588  -0.000244137  6.27183e-9  0.0
+8×8 LowerTriangular{Float64,Array{Float64,2}}:
+  0.476444     ⋅           ⋅            ⋅            ⋅             ⋅            ⋅           ⋅ 
+ -0.0495227   0.102521     ⋅            ⋅            ⋅             ⋅            ⋅           ⋅ 
+ -0.0557742  -0.0170701   0.102316      ⋅            ⋅             ⋅            ⋅           ⋅ 
+  0.0295214  -0.0165868   0.0781059    0.108318      ⋅             ⋅            ⋅           ⋅ 
+  0.0292097  -0.110967   -0.0943707    0.00550319   0.0            ⋅            ⋅           ⋅ 
+  0.0319541  -0.0243266   0.00505476  -0.0540444    0.000111037   0.0           ⋅           ⋅ 
+ -0.0139336   0.0126983  -0.0135029   -0.134248     9.89607e-5    0.000144849  0.0          ⋅ 
+ -0.0463229   0.0218126  -0.0650083    0.0516112   -0.000120772  -0.000171985  1.49074e-5  0.0
 
 ````
 
 
 
 ````julia
 julia> mm1.trms[2].Λ
-8×8 Array{Float64,2}:
-  0.570451     0.0          0.0         0.0         0.0         0.0          0.0         0.0
- -0.0233509    0.0639696    0.0         0.0         0.0         0.0          0.0         0.0
- -0.267494    -0.288241     0.0411303   0.0         0.0         0.0          0.0         0.0
-  0.0174073    0.00128561  -0.0300041   0.07846     0.0         0.0          0.0         0.0
-  0.0289346   -0.0302377   -0.0137795  -0.0102507   0.0234571   0.0          0.0         0.0
-  0.0178525    0.00360149  -0.0247621   0.0172816  -0.0529219   0.00277857   0.0         0.0
-  0.00842305  -0.0252118    0.0957016   0.0193387  -0.0391965  -0.00149982   0.0         0.0
-  0.00494545  -0.050996     0.0127431  -0.0779396   0.0569404  -0.00147603  -4.42426e-5  0.0
+8×8 LowerTriangular{Float64,Array{Float64,2}}:
+  0.569675      ⋅            ⋅            ⋅             ⋅           ⋅            ⋅           ⋅ 
+ -0.0234122    0.0640206     ⋅            ⋅             ⋅           ⋅            ⋅           ⋅ 
+ -0.266913    -0.288127     0.0425733     ⋅             ⋅           ⋅            ⋅           ⋅ 
+  0.0173413    0.00329602  -0.0139551    0.0829213      ⋅           ⋅            ⋅           ⋅ 
+  0.0290032   -0.0307006   -0.0162798   -0.00678668    0.0226446    ⋅            ⋅           ⋅ 
+  0.0178621    0.00437284  -0.0184925    0.0223168    -0.0535127   0.00364195    ⋅           ⋅ 
+  0.00844082  -0.0241439    0.0991966    0.000985977  -0.0355039  -0.00381326   0.0          ⋅ 
+  0.0049074   -0.053426    -0.00479098  -0.0775749     0.0560694  -0.00114592  -5.49465e-5  0.0
 
 ````
 

diff --git a/docs/src/constructors.md b/docs/src/constructors.md
@@ -11,15 +11,28 @@ lmm
 For illustration, several data sets from the *lme4* package for *R* are made available in `.rda` format in this package.
 These include the `Dyestuff` and `Dyestuff2` data sets.
 ````julia
-julia> using DataFrames, RData, MixedModels
+julia> using DataFrames, RData, MixedModels, StatsBase
 
 julia> const dat = convert(Dict{Symbol,DataFrame},
     load(Pkg.dir("MixedModels", "test", "dat.rda")));
 
-julia> dump(dat[:Dyestuff])
-DataFrames.DataFrame  30 observations of 2 variables
-  G: DataArrays.PooledDataArray{String,UInt8,1}(30) String["A", "A", "A", "A"]
-  Y: DataArrays.DataArray{Float64,1}(30) [1545.0, 1440.0, 1440.0, 1520.0]
+julia> describe(dat[:Dyestuff])
+G
+Summary Stats:
+Length:         30
+Type:           CategoricalArrays.CategoricalString{UInt8}
+Number Unique:  6
+
+Y
+Summary Stats:
+Mean:           1527.500000
+Minimum:        1440.000000
+1st Quartile:   1468.750000
+Median:         1530.000000
+3rd Quartile:   1575.000000
+Maximum:        1635.000000
+Length:         30
+Type:           Float64
 
 
 ````
@@ -67,7 +80,7 @@ The second and subsequent calls to such functions are much faster.)
 
 ````julia
 julia> @time fit!(lmm(@formula(Y ~ 1 + (1|G)), dat[:Dyestuff2]))
-  0.000860 seconds (1.40 k allocations: 75.156 KiB)
+  0.000941 seconds (1.44 k allocations: 74.375 KiB)
 Linear mixed model fit by maximum likelihood
  Formula: Y ~ 1 + (1 | G)
    logLik   -2 logLik     AIC        BIC    
@@ -141,7 +154,7 @@ Linear mixed model fit by maximum likelihood
 
 Variance components:
               Column    Variance  Std.Dev.   Corr.
- G        (Intercept)  584.258968 24.17145
+ G        (Intercept)  584.258971 24.17145
           U             33.632805  5.79938  0.00
  Residual              653.115782 25.55613
  Number of obs: 180; levels of grouping factors: 18
@@ -511,10 +524,10 @@ sdest
 ```
 ````julia
 julia> varest(fm2)
-654.9414511016189
+654.9414530367545
 
 julia> sdest(fm2)
-25.591823911195128
+25.591823949002823
 
 ````